I have Etymotic ER4 noise isolation and the ever-popular Bose QC3 noise cancelling. I like them both but for different reasons.

Noise Isolation
+ small enough to put in your pocket
+ good to use on subway / metro etc
+ no batteries
+ decent sound quality

- if I move around (walking for example) I can "hear" the headphones; i.e. I get this "thump thump" sound as my feet hit the pavement. It's extremely annoying and to me, it makes the headphones useless unless I'm sitting down in an airplane or on the metro
- sound quality is decent but not as good as my Bose. I often wonder if the Shure will sound better than Etymotic but I've never tried them
- After 5+ hours, I find it hurts to have something stuck in my ears
- The noise isolation works basically by inserting a small sound tube surrounded by a thin rubber membrane. Although this doesn't happen often, air pressure changes on an airplane can be frightfully difficult to deal with when your inner ear is isolated from your surroundings by a thin rubber membrane. The solution of course is to remove the headphones, but even at cruising altitude this can be an occasional annoyance.
- Noise isolation works well, but I find that I do have to turn the volume a little higher then with my noise cancelling. It's possible this is an efficiency thing (impedence of the headphones for example)

Noise Cancelling
+ Generally pretty good sound
+ I find that the QC3 on-ear design is less bulky than the QC2 and QC1 over-ear design
+ The (rechargeable) battery lasts a long time. I've flown YYZ - HKG (17h) without difficulty
+ The noise cancellation works very well. As a result, I don't have to turn the volume of my iPod very high. Clearly this is better long term for my ears.

- The QC3 uses a battery. Like all batteries I'm sure this one will die eventually. Like all batteries it will die at a moment I'm not near a (Bose) battery store.
- Design is still bulky. This is not a headphone I would use casually; just on airplanes really.
- Although the noise cancellation is great, it does (for me and evidently for Arthurrs above) generate some fatigue. I can't listen with these headphones for longer than 4 - 5 hours without feeling tired.
- Both the on-ear design of the QC3 and the over-ear design of the QC2 slightly squish my ears closer to my head. As such, after 4 - 5 hours of listening my ears hurt a little.


In the end, I'm glad I have both Bose noise cancelling and Etymotic noise isolation. On long flights, I always start with my Bose, but typically (after 4 - 5 hours) switch to the Etymotics for a bit, then back to the Bose. For short hops I just take the Etymotics as they fit easily into a pocket.